Repro steps:
1) Open the project and scene 'Bake from Script'
2) Press Build in the Lighting window - notice it builds fast
3) In the menu bar click Lighting Test -> Bake Lightmaps...
4) Notice it increases Indirect Resolution instead of Baked Resolution in the Lighting window's Baked GI part, which causes tremendous increase in Build time

Workaround: set default values in the Lighting window and do not change them through script

Reproduced in: 5.4.0b1; 5.3.1p2; 5.2.3p3